Jeffrey Sinclair, former commander of Babylon 5, is appointed Earth Alliance ambassador to the planet Minbari. Although on the surface the Minbari appear to be co-operating with him in his role, in practice they are being very unhelpful, preventing him from contacting the Earth government, and from doing some of his duties as ambassador. Eventually Sinclair is taken to a meeting by the head of the Grey Council to meet with Delenn, Kosh Naranek, and Ulkesh Naranek, where they reveal that they believe Sinclair possesses part of the soul of their historic saviour Valen from the previous Shadow War 1,000 years ago. They wish Sinclair to lead Vorlons and the Minbari in the fight against the Shadows. They give Sinclair the title Entil'Zha (or "The One Who Creates The Future") and ask him to reform their Rangers warriors, who fought in the previous war. Sinclair insists that humans are allowed to join the Rangers, and he is advised that they must learn to fight using the Minbari Fighting Pike (the Denn'Bok), as well as regular military training. Among the members he recruits are Marcus Cole and his ex-girlfriend Catherine Sakai, who he rekindles his relationship with.

Catherine quickly becomes a teacher to the Rangers, and their best pilot. When Sinclair is informed that the Shadows, and their minions, are trying to create a time rift to send their forces back in time to win the previous Shadow War. Sinclair assembles a team, including Catherine and Marcus, to prevent them. They succeed in their mission, but Catherine is captured in the time rift and is sent to an unknown time. Sinclair returns to Minbari where he receives a letter from 1,000 years ago from Valen himself, in this letter it is revealed that Sinclair must use a chrysalis machine to transform himself into a Minbari, and become Valen. Sinclair must take Babylon 4 back in time, with Zathras, where he will win the previous Shadow War, as well as reorganizing the Minbari caste system, creating the Grey Council and forming the original Rangers. Sinclair asks Kosh, if he does this, will he meet Catherine again, who replies "Perhaps".